Monday, October 31, 2011

Origin of Kalash inferred with Eurogenes K=10 "test" calculator

Vasishta, is asking Eurogenes for help in demonstrating that the Kalash have Northern-European-specific segments:

Yes. He keeps citing the Kalash as proof that the Indo-Iranians were an almost exclusively a West-Asian like population, even though I personally think the mainly West Asian-South Asian assortment of the Kalash in his analyses might be an artifact of their inbreeding and isolation, thus confusing ADMIXTURE. Zack's K=11 at Harappa has shown that the Kalash display around 22% of the component modal in Lithuanians. Yet, he ignores the North/Eastern European admixture in Northwest Indians and North Indian Brahmins (in his own analyses at that!). Interestingly enough the aforementioned groups tend to score a sliver of Northeast European admixture in Dr.Doug McDonald's analyses, with the top matches for that sliver usually being Lithuanians, Russians and Finns; in that order. It (NEU) is even found in frequencies of around 4-6% in Dravidian-speaking southern Brahmins. As much as I hate to say it, he is indeed rather stubborn and has somewhat of an underlying agenda.

David, I think you should look into proving that the Kalash do indeed have some NEU-specific segments. I would be super-surprised if they didn't, given that more mixed populations south of their geographical area display it themselves.

It appears that Vasishta disagrees with me because he "personally thinks" that the admixture proportions of the Kalash are due to inbreeding and the limitations of ADMIXTURE.

Does he cite any studies or make any argument why ADMIXTURE would remove precisely the component that he is so eager to be present? No. While genetic drift in an isolated population could indeed lead to the loss of genetic diversity, there is no reason to think that this would lead preferentially to the loss of Northern-European segments. It is strange that Vasishta accuses me of bias and yet, at the same time, invokes the magic of some unspecified flaw of ADMIXTURE for the loss of his favorite component.

Vasishta invokes the Harappa Ancestry Project K=11 admixture analysis in support of his idea that the Kalash have 22% of the component modal in Lithuanians. However, he neglects to mention that at K=11 there is no West-Asian or Caucasus centered component in the HAP analysis, but rather only "European" (modal in Lithuanians) and "SW Asian" (modal in Yemen Jews). It is indeed strange that he accuses me of bias for providing evidence about the relationship of the Kalash with West Asia, while at the same time, showing preference for a level of analysis where such a component is lacking.

The West Eurasian cline between Arabia and Northeastern Europe is evident in the 'weac' admixture analysis, where the European-centered component (Atlantic-Baltic) is present in populations such as Assyrians and Armenians whereas it is lacking at the appropriate level of resolution. Therefore, the fact that the Kalash show "European" admixture at the level of Europe vs. Near East does not mean that they ought to show such admixture at the level of Europe vs. West Asia/Caucasus vs. Arabia.

One of the benefits of DIYDodecad has been the availability of data from projects that have hitherto been black boxes. In the interest of transparency, I have taken the Eurogenes K=10 "test" calculator and repeated my analysis of the Kalash, that had been previously shown byme to be a fairly simple West/South Asian mix. I could have waited for him to get around to it, but since he's quick on the talk and slow on the trigger, I decided to do it for him.

The admixture proportions of the Kalash, according to the Eurogenes K=10 are: 40.3% S_Asian, 58.7% W_Asian, 0.9% N_E_Euro, 0.1% N_Asian, and hence the analysis based on the Eurogenes K=10 components confirms the analysis based on my eurasia 7, "showing the Kalash to be a "West Asian" population (62.4%) with substantial "South Asian" admixture (37.1%), and near-complete absence of any other genetic components."

Eurogenes alleges, not without his usual charm, that:

Dienekes has a keen eye for things he wants to see. But he hasn't yet noticed that in all accurate analyses, there's significant Eastern European admix in North India. His monocle got fogged up in that instance.

Let us consider some pertinent facts: the Indian peninsula has been invaded multiple times from Central Asia, a process that continued long after the establishment of the Indo-Aryans during the 2nd millennium BC. Eurogenes may want to think that the "Eastern European" admixture in South Asia dates to his mythological Polish Indo-Europeans, galloping across the steppes on their horses, but there is, at present, no particular reason to think that this is the case

Furthermore, the "West Asian" component as a fraction of the "West Asian" + "Atlantic-Baltic" component reaches a minimum of 77% in the Pathans in populations from the northern parts of the Indian subcontinent. His own monocle is surely in greater need of de-fogging if I miss the 23% and he misses the >77%.

Indeed, the Europe vs. Caucasus ratio in Indian subcontinental populations is similar to that found in people from the Middle East and Caucasus region. It is not surprising that Eurogenes has abandoned his search for North European components in South Asia, going as far as reconstructing Ancestral North Indians as "Northern Europeans". Needless to say, he waswrong. The West Eurasian ancestry of the population of the Indian subcontinent is similar to that found in modern West Asian populations, not Slavs.

Eurogenes promises:

This shouldn't be too difficult. I'll use Dienekes' calculator for the job, and then check the results with LAMP.How poetic.

Been there, done that. It will be fun to see what "Northern European" components he will be able to squeeze out of the 0.9% N_E_Euro component that my software, in conjunction with his "test" calculator produces.

Why are the Kalash important?

There are three reasons why the Kalash are important in the study of Eurasian prehistory:

Their mountainous habitat contributed to isolation and relative immunity from historical population movements

Their non-Islamic religion has definitely preserved them from recent gene inflow

Their language is unique within the Indo-Aryan family, and it often considered today as part of a separate Dardic family of Indo-Iranian in addition to the more populous Iranian and Indo-Aryan families.

The Kalash are crucial for those interested in the origins of Indo-Iranians, and the fact that they are, indeed, a simple West/South Asian mix is not without significance for that question.

UPDATE:

Here is the result of a PCA analysis of the Kalash together with 50 synthetic individuals from each of the S_Asian, W_Asian, and N_E_Euro components of Eurogenes K=10 "test". This was calculated with smartpca with numoutlieriter set to 0.

It is evident that the Kalash appear to fall on the S_Asian to W_Asian line, and toward the W_Asian pole, consistent with being a population of those two origins, with the W_Asian component predominating.

UPDATE II:

As mentioned in the eurasia7 post, the Kalash tend to form population-specific components in ADMIXTURE analyses, so they are generally not included in my runs. So, I run the K=7 analysis again, but this time I included the Kalash. Here are the top populations of the component that was modal in the Kalash:

[186,] "Kurd_D" "50.2"

[187,] "Kurds_Y" "50.7"

[188,] "Armenian_D" "50.9"

[189,] "Armenians_Y" "51.2"

[190,] "Adygei" "51.5"

[191,] "Chechens_Y" "53"

[192,] "North_Ossetians_Y" "53.2"

[193,] "Lezgins" "54.4"

[194,] "Georgians" "59.8"

[195,] "Georgian_D" "60.1"

[196,] "Abhkasians_Y" "60.5"

[197,] "Kalash" "63.2"

Here are their exact admixture proportions in this unsupervised ADMIXTURE run:

Kalash N=23

East_Asian: 0.5

Atlantic_Baltic: 1.5

South_Asian: 32.9

Sub_Saharan: 0.0

Southern: 0.0

Siberian: 1.8

West Asian: 63.2

UPDATE III (November 22): Eurogenes estimates that there is 4% "Northeast European" admixture for Kalash individual HGDP00302. He managed to avoid the creation of a Kalash-specific component by including only a single Kalash individual in an ADMIXTURE experiment.

The Kalash do tend to create their own Kalash-specific component, and a good way to avoid such a component is to include each of them individually, and repeat the analysis 23 times. An alternative, and less time consuming way, is to create a single synthetic individual using the allele frequencies of the Kalash population as a whole. Even simpler, one could randomly pick a single individual (such as HGDP00302), but at the risk of picking an individual that has either much more or much less than average a particular type of ancestry.

Below are the admixture proportions of all the 23 Kalash individuals from the unsupervised ADMIXTURE run of UPDATE II. Individual HDGP00302 is 4th of 23 in terms of their "Atlantic_Baltic" component that peaks in Lithuanians (3%). The Kalash have 1.5% "Atlantic_Baltic" on average (median=1%, standard deviation=2.1%).

You made a mistake, there is no "N_Euro" cluster in that Eurogenes run. I assume you mean N_Asian.

Anyway, regardless of whether the Kalash happen to lack North/East European affinities when a West Asian component is inferred by ADMIXTURE, we also know that other South Asians, from areas deep into the subcontinent, show appreciatable amounts of North/East European in addition to West Asian and South Asian. This is clear in the Eurogenes K=10 calculator, but this result is not exclusive to Eurogenes.

So I believe it is dubious to disregard the possiblity that North/East European affinities in Indo-Aryan populations could tell us something about the origins of the Indo-Aryans. That is not to say that the higher West Asian in Indo-Aryan populations and certain castes is of no importance, that is indicative as well.

>> Dieneke what is the ASI to ANI ratio score of the Kalash in South Asian component (Thats if you are using ANI and ASI)? Compared to west Iranians?

Well, Reich et al. (2009) did not measure their ANI/ASI ratio. Also the Kalash are more West Asian than Pathan/Sindhi (two of the most West Eurasian-admixed populations used by Reich), so it's not, strictly speaking possible to infer their ANI/ASI ratio by extrapolating from the Indian Cline populations, because the Kalash are "off cline".

@Lank, thanks for the correction.

I don't disregard the "possibility". Anything is possible. But, there are many factors arguing against that. For example, French_Basque and Finns, the two major non-IE populations of Europe lack the "West Asian" component that their IE-speaking neighbors possess.

Dienekes, my post wasn't meant to be some sort of defamation or slandering exercise of your work. I'm actually quite a big fan and I've cited your blog posts a number of times in forum discussions. I agree with the fact that the HAP K=11 isn't the ideal analysis to cite in order to reflect on the possible Northern European admixture of the Kalash since there is neither an exclusively West-Asian or Northeast European centered component in that specific run. But even in your initial K=10 analysis, the Northern European component was found in non-trace amounts in many of your Indian_D samples.

The migration of later, historic migrations of Central-Asian groups such as the Parthians, Scythians/Sakas, Kushans and Hephthalites into the subcontinent does not exactly explain the presence of the Northern European modal component across different ADMIXTURE runs in castes such as the Brahmins, who have historically been very endogamous and deemed outsiders, even other Indo-Iranian groups, as mlecchas. Even the south Indian Brahmins of your project exhibited Northern European (initial K=10), North Eastern European (subsequent K=12, not the v3 one) and the Atlantic_Baltic (eurasia7) components, varying between 4-7% roughly in each run; leave alone Northwest/North Indian Brahmins who have it at even higher levels. My statement was motivated by the fact that the presence of Northern European admixture in non-trace amounts in the least West-Eurasian of upper caste groups (i.e Dravidian-speaking Brahmins of southern India) just doesn't match up with the absence of it in a group that is often hypothesized as an Indo-Aryan relic population (i.e, the Kalash).

Also, just to clarify - the NEU component isn't some sort of pet component of mine. Subjectively speaking, a while ago, I wouldn't have liked anything better than Indo-European origins being proved to have it's ultimate origins in West Asia. But populations genetics has compelled me to set aside biases, notions of cultural superiority and personal preferences and think more objectively. And a constant signal I'm seeing across the analyses of genome blogger projects is the presence of Northern European admixture in groups that traditionally claim Aryan descent. For instance, south Indian Brahmins are distinguished from their non-Brahmin counterparts by the presence of N European admixture in non-trace amounts. Other south Indians in general seem to completely lack it.

I did not intend to offend you, and I am sorry if I came across that way in the spur of the moment. If genome bloggers such as yourself are going to cite me as the cause of some sort of potential defamation of their work in light of a rather casual statement during a discussion on some anthropology forum, I don't know if I should post in these fora anymore.

As for South Indian Brahmins, they do NOT trace their origin in South India at the time of the Indo-Aryan migration

http://en.wikipedia.org/wiki/Tamil_Brahmin

"There have been evidences of Brahmin presence in the southern states even prior to the Sangam Age. However, it is generally believed that they were few in number and that most Iyers migrated from other parts of India at a later stage. According to P. T. Srinivasa Iyengar, the sages Apastamba and Baudhayana whose sūtras or legislations are followed today by Tamil Brahmins lived in the Telugu-speaking territories to the immediate north of the Tamil country even before the Sangam period.[2] The 2nd century AD literary work Paṭṭiṉappālai written by the Brahmin poet Uruttirangannanar (Kannan, son of Rudra) records the presence of Brahmins and Vedic rites in Karikala's kingdom. The Akanaṉūṟu refers to a vela-parppan or a Brahmin who does not perform Vedic sacrifices. Similarly, other literary works of the Sangam period like the Silappatikaram, Manimekalai and Kuṟuntokai also allude to the presence of Brahmins in the Tamil country. The influence of Brahmins and Indo-Aryan culture, however, began to grow rapidly only during the last centuries of the Sangam period."

There is no reason, therefore, why the presence of the N_E_Euro component in them should be difficult to explain, as their southward migration long postdates the Indo-Scythian migrations into India.

As for the supposed lack of intermixture between Brahmins and outsiders, this is contradicted by the fact that South Indian Brahmins _do_ differ from North Indian Brahmins, and occupy different positions along the Indian Cline, consistent with differential admixture of non-Brahmin elements.

Brahmin purity rules definitely indicate that this population has a higher degree of Indo-Aryan origin than some other Indian caste groups, but it does not preclude the absorbtions of non-Aryan elements of both domestic and foreign origin.

I wasn't asserting that Brahmin groups in India are somehow free of non-Brahmin admixture. The very fact that Dravidian-speaking Brahmins occupy a position between south Indians and Pakistanis speaks volumes with regards to admixture with the local substrate, perhaps only until a certain period of time post their initial migration to south India, which might be the explanation for their genetic homogeneity. There is and was obviously a higher propensity to acquire indigenous as opposed to exogenous elements. What I am asserting is, that the intrusions of West-Eurasian populations from Central Asia and the like are unlikely to be the cause of the presence of Northern-European specific alleles in upper caste Hindus and also Northwest Indians for the most part (although the likely hood of the impact of these intruders is probably comparatively more in this area).

The component in question is probably more ancestral and ancient in nature. I'd like to continue this discussion tomorrow or so, with a clearer head to address the other points you've brought up.

obviously there is some of both. the question is how much. the presence of a central eurasian variant of LCT in northwest india suggests at least some contact with northeast european/kurgan populations (or lots of later scythian intrusion). but overall the dominance of a west asian element to me is suggested by phenotype. there's just not enough light eyvariants segregating in south asians. of course this could be an artifact of selection. though strangely it didn't happen with slc24a5, which is found at proportions pretty much tracking "ANI" (it's nearly fixed outside of europe among west asians).

OK, in the end, we're all looking for the same thing, which is the most accurate picture of the past. So let's ask ourselves honestly how we can do that, so that no one can level any claims of bias against any of us.

Dienekes, maybe the best solution here is to try and run the five most outbred/differentiated Kalash in the same analysis, and then see whether their components differ from their supervised results?

If they don't differ, then you're right. If they do differ, then something's off, and a solution must be found, because supervised tests are indeed useful if accurate.

Continuing from where we left of yesterday, I highly doubt that the Hindu priestly castes could have acquired any foreign West-Eurasian elements post the initial Indo-Aryan expansion. This doesn't fit into any known historical context. There is no mention of Brahmins intermarrying with non-South Asian Indo-Iranian groups in any of the ancient texts.

I think it is far more likely for the generic denizens and in addition, the ruling class to have absorbed such elements, in Northwest India, the area most of these people entered the subcontinent from. For instance, in the Mahābhārata; Gāndhārī, who is the wife of the Kuru king Dhritarāshtra (the kingdom of the Kurus was mainly situated in present day Delhi, Haryana and Western Uttar Pradesh) was the daughter of the king of Gandhara. Her brother was Shakuni was known as Gandhar-naresh (naresh = king, in this context).

The Jatt participants of both the Dodecad and Harappa Ancestry Project have elevated amounts of Northern European admixture relative to other Punjabi speakers, which might well suggest actual and real Scythian admixture (although not their predominant ancestry). DOD089, DOD090, DOD091 and DOD0736 are Jatts from Punjab. DOD0746 and DOD0832 are Jatts from Haryana, in Northwest India. They exhibit the component in question as much as the Pashtun reference samples do, and sometimes even more than the Pathans, which is interesting given their geographical location. This has been mentioned elsewhere, but it is relevant to mention it here - it would indeed make far more sense for a peasant/farmer/baron caste like the Jatts to have been historically more willing to mix with foreigners, who would otherwise be deemed as mlecchas by the Brahmins. Furthermore, many of the names of Jatt clans are reminiscent of ancient Scythian tribe names. Here is a post/comment on the HAP blog on that.

In conclusion, I am rather doubtful of the proposition that any Northern European admixture in South Asia post dates the initial Indo-Aryan expansion.

I highly doubt that the Hindu priestly castes could have acquired any foreign West-Eurasian elements post the initial Indo-Aryan expansion.

I don't doubt it one bit. We have a very good example: Jewish Cohanim, whose origin also dates to the 2nd millennium BC, and who also guard their status jealously on genetic grounds. Nonetheless, there is an assortment of different lineages that have crept into that gene pool over the millennia.

The Jatt participants of both the Dodecad and Harappa Ancestry Project have elevated amounts of Northern European admixture relative to other Punjabi speakers, which might well suggest actual and real Scythian admixture

Correct, and consistent with my claim that this elements represents Indo-Scythian ancestry to a substantial extent.

We know for the fact that Saka-type people entered India and set up kingdoms there. We also know for a fact that they did not keep their old religion but were incorporated into the Hindu fold. More likely than not, they intermarried with local Hindus at all levels of the caste hierarchy.

No matter how rigid the caste hierarchy is supposed to have been, it is indubitable that intermarriage across its lines was prevalent in the past; otherwise modern-day caste groups would not span the length of the Indian cline. Some level of admixture with foreigners, especially those in a position of power is all but certain.

@ Dienekes How do you explain that the South Asian component is closer to Atlantic-Baltic than to the Southern component?How do explain that the South Asian component also appears far away from South Asia in Northern Africa (1-5%), in the Baltic region (3-4%), and in Yemen (6%)?

How do you explain that the South Asian component is closer to Atlantic-Baltic than to the Southern component?

The South Asian and Atlantic-Baltic components are closer to the West Asian one, rather than the Southern one, because, I believe, they have both sprung (partially) from a common source somewhere in the northern parts of West Asia.

The Southern component appears to be an earlier offshoot from the Near East, as evidenced by its substantial presence north/south and east of the Mediterranean, and its higher Fst distances to the rest.

My default hypothesis based on the available data is that the R1 clade has its origins in the vicinity of the Caspian, with R1a showing a distribution on the long arc along the flatlands north and east of the Caspian, and R1b in the complementary "short arc" of the highlands west and south of it.

The latter has to be "east enough", otherwise it would have been involved in migrations from Anatolia/Levant during the early Neolithic, but also "west enough" otherwise it would have been present in South Asia.

In the old days of of physical anthropology and linguistics the idea of a special kinship between Northwest Europeans and the people who brought an Indo-European to South Asia was widely accepted. For example, "the Indo-European languages were, at one time, associated with a single, if composite, racial type, and that racial type was an an ancestral Nordic" (C. S. Coon "The Races of Europe" p.221). How the older anthropologists and linguists came to this conclusion is not clear to me. Coon was aware that the skeletons he identified as Nordic were very similar to Southwest Asian highlanders.

"How the older anthropologists and linguists came to this conclusion is not clear to me. "

The British physical anthropologists started with this idea.

The same British physical anthropologists stated that Britain is predominantly "Nordid" in physical phenotypes and by this, close to the Indoeuropean invadors, who "subdued" allthe inferior races of Europe...and by this, are the "Master Race". What a surprise. ;)

Well, as far as I recall, the claim is, that the skulls of the anchestral Europeans (the natives) are all brachycephalic and broad faced.The bones massive. Giant, muscular brutes.

And in the late neolithic, there suddenly apear gracile, tender boned, dolchiocephalic and slim faced people and spread all over the place.

Those old maps claim, people of modern day SPain, Portugal, Britain, Ireland, Netherland, Denmark, Norway, Sweden, South Finland, Estonia, Latvia and Lithuania fit those new comers phenotypes best while France, Soutgermany, Switzerland, Astria, North Italy and north Balkans apear to be closer to the (of course racial inferior *Sarcasm*) native Europeans. So much for the "Old School" view of British style physical anthropology.

Strange however, that the mtDNA of the Baltic countries is suposedly closest to native European one. Followed by Scandinavia. 2 places that are, by physical anthropology, most close to the late neolithic arrivers who had been connected to the Indoeuropeans by 1930s science.

Dienekes said : "I don't doubt it one bit. We have a very good example: Jewish Cohanim, whose origin also dates to the 2nd millennium BC, and who also guard their status jealously on genetic grounds. Nonetheless, there is an assortment of different lineages that have crept into that gene pool over the millennia."

Instead of providing a parallel, I'd like to see some actual and relevant evidence based on scriptures and other texts that the Brahmins intermarried with foreigners such as the Sakas. There is absolutely mention of this in any of the ancient texts. Intermarriage with mlecchas is most plausible for the other upper castes to an extent - Kshatriyas (politically motivated), Vaishyas (trade) and the non-upper castes such as agriculturalists, but I seriously doubt the North Euro admixture among Brahmins is an artifact of the Sakas instead of the initial Indo-Aryan expansion. Also, the reason I initially cited HAP's K=11 Ref 3 analysis is because it is maximally informative for South-Asian populations. The South-Asian cluster in Harappa K=11 is predominantly West-Eurasian, so it's mostly specific to ANI. The Onge component covers the bulk of ASI while the remainder of the non-West Eurasian part of the South-Asian component covers for the rest. Here's a PCA plot which compares the South-Asian component at Ref. 3 K=11 (labeled sa11), with the old South Asian component from the initial HAP K=12 Ref.I/Ref.II runs (labeled sa12), which is more similar to the South-Asian component seen in Dodecad K=10 and dv3 K=12. As an aside, Zack posted an update today at the HAP blog with a new set of ADMIXTURE runs. See - Ref3 + Yunusbayev Caucasus Data Admixture. He mentions that the lowest crossvalidation errors are for K=17 and K=12. At K=12, here are the ADMIXTURE proportions for the Kalash - West Asian - 71%South Indian - 14%Northern European - 10%SE Asian - 3%NE Asian - 1%American - 1%

Okay, so there is both a West-Asian and Southern European centered component here which filter out any spurious clusters that may overestimate admixture scores and peg alleles accurately. To add to that, Zack's data-set is perhaps the most extensive from a South-Asian perspective. So, what's up with that 10% North Euro score in the Kalash?

The evidence that Brahmins intermarried with foreigners in their genes: they have absorbed a substantial quantity of native South Asian ancestry. It is somewhat ridiculous to think that the Indo-Aryans would intermarry with indigenous South Asians to a huge extent, but would maintain their racial purity vis a vis subsequent waves of Central Asians, especially since those found themselves at the top echelons of society.

Moreover, this admixture continued long after the initial arrival of the Indo-Aryans in India, as evidenced by the fact that different Brahmin groups occupy different positions along the Indian cline.

I'm sorry that you want to trace your favorite North European component to the time of the Indo-Aryans, but there is really no evidence that that is the case.

At K=12, here are the ADMIXTURE proportions for the Kalash - West Asian - 71%South Indian - 14%Northern European - 10%

The "West Asian" component is mislabeled, as it is most prevalent among the Kalash, with West Asians following at a great distance. It is a Kalash-specific component that is not completely resolved, something which occurs at K=13.

It is incorrect, since the "West Asian" component at K=12 is actually a partially resolved Kalash component.

The Kalash are at ~60% West Asian ~40% South Asian according to both eurasia7 and 'test'. The partially resolved Kalash component makes them appear to be ~70% "West Asian", i.e., 10% more "West Asian" than they really are in the latitudinal North European/West Asian cline in West Eurasia, and with the addition of 10% "North European" they go to their correct place (60% West Asian)

To add to that, Zack's data-set is perhaps the most extensive from a South-Asian perspective.

That is irrelevant, since the issue in question is the correct resolution of the West Asian component/ This is correctly resolved in the unsupervised run of the Dodecad Project (Update II), probably because of the much greater number of West Asian samples in the Dodecad Project, which prevent a Kalash-specific component to emerge too soon. By contrast, there is never any West Asian component that emerges in the HAP, and the analysis goes from a "SW Asian" component to a partially resolved Kalash component, and then to a fully resolved Kalash component.

Right. It looked a little odd to me as well that the West-Asian component was modal in the Kalash. Thanks for the explanation, Dienekes. Again, there's no need to subtly ridicule me by asserting that the component we're debating about here, is somehow my favorite component, as I've always thought that the consistency of the presence of North Euro admixture in South-Asia (Northwest South Asia and upper caste Hindus in general) did in fact point out to the fact that it was a secondary element among the Indo-Iranians, with the elevation of it among the Jatts in particular being partially attributed to the absorption of a Scythian substrate. Anyway, my confidence is all this is rather low until we can somehow date the admixture events, even the components that are revealed upon a more granular analysis of the ANI ancestry of South-Asians.

" I don't disregard the "possibility". Anything is possible. But, there are many factors arguing against that. For example, French_Basque and Finns, the two major non-IE populations of Europe lack the "West Asian" component that their IE-speaking neighbors possess."

The while the basques have less west Asian than thrir surrounding IE speaking neighbors they ALSO have less NEU than their IE speaking neighbors.

The finns do in fact have some west Asian and they actually have more west Asian than the nearby IE speaking Lithuanians, which is inconsistent with a west Asian people spreading IE in Europe. On the other hand the Lithuanians do have more NEU than the close-by non IE speaking finns.

Lastly the Lithuanians have a very small amount of west Asian relative to the whole of Europe, even less than the Spanish, despite the fact that they speak an IE language and are closer to the IE homeland.

In summary the WA theory explains the WA dip in the basque but it does not explain the WA dip in Lithuania relative to Finland. The WA theory also doesn't explain why the Lithuanians have so little WA.

The NEU theory explain the basque in relation to their neighbors, the finns in relation to the Lithuanians, and the Lithuanias in relation to Europe.

The while the basques have less west Asian than thrir surrounding IE speaking neighbors they ALSO have less NEU than their IE speaking neighbors.

I don't know where you are getting this from, since there is no "NEU" in euro7. If you are referring to the "Northeastern" component, the French_Basque sample has 0.4%, while Spaniards, Spanish_D have 2.2-2.5%, not a particulary significant difference..

The finns do in fact have some west Asian and they actually have more west Asian than the nearby IE speaking Lithuanians, which is inconsistent with a west Asian people spreading IE in Europe. On the other hand the Lithuanians do have more NEU than the close-by non IE speaking finns.

Again, there is no "West Asian" on euro7, so I don't know what you are talking about. In eurasia7 where there is such a component, FIN ha s 1.8%, Finnish_D 1.6%, Russian 8.7%, Swedish_D 5.5%, Lithuanians_D and Lithuanian 5.1-6%.

Lastly the Lithuanians have a very small amount of west Asian relative to the whole of Europe, even less than the Spanish, despite the fact that they speak an IE language and are closer to the IE homeland.

Finns, French_Basque have even less. Lithuania adopted a Neolithic economy very late in the game, and Indo-European speech at least that late. Also, the ancient DNA evidence suggests that populations from the eastern Baltic have the most amount of influence from northern Mesolithic hunters and fishermen of the PWC, who were certainly NOT any type of Indo-European

In summary the WA theory explains the WA dip in the basque but it does not explain the WA dip in Lithuania relative to Finland. The WA theory also doesn't explain why the Lithuanians have so little WA.

Because there is no such dip, but rather a small difference in the opposite direction.

In the K=12 v3 French Basques show a bit more West Asian than Lithuanians, and some Iberians whose heritage is mostly from the Northeast, lack the component, sometimes even without Southwest Asian too.

It's curious that at higher resolution (in comparison with the Eurasia7) we find it increased between Basques.

Do you think the ptoto Indo-iranians (Andronovo people) were Z283 carriers from Poland/Russia who brought technology(and slavic vocabulary) and imposed their language on z93 carriers in south-central asia. I saw this theory circulating on the web.

1. I don't think Andronovo has anything to do with Proto-Indo-Iranians. Rather, the Proto-Indo-Iranians formed in the territory of the BMAC.

2. I see no evidence for the scenario you are describing. The dust needs to settle on the new discoveries within R-M17 to make a complete case, but Z93+ seems to be shared by people in Central Asia, India and Iran, so if any type of R-M17 was present in early Indo-Iranians (which seems likely), Z93+ seems like a good bet.

I think the Indo-iranian formed in the territory of the BMAC but Andronovo seems to be associated with the Proto Indo-Iranians by many people doesn't it.

It's not based on anything. There is no evidence for any Indo-Europeans on the steppe before the 1st millennium BC. Even in historical times when Iranic nomads are on the steppe, these represent a small twig of the Indo-Iranian tree (=a branch of Iranian), hardly what we'd expect if the steppe was the Indo-Iranian homeland.

Those people had to go somewhere and there seems to have been contact between Andronovo and BMAC tribes.

They didn't have to go anywhere, because they lived just fine on the steppe along with their goats and other livestock.

If we had to wonder about something is what happened to the huge population of the BMAC that could no longer live there due to climate change in the 2nd millennium BC. The exodus of that population is just what we'd expect for the breakup of Indo-Iranian

Also what would explain the North Eurasian component in Afghanistan/Pakistan. And why is it mostly Western btw?

These regions have been settled by Iranic speakers throughout history. All genetic evidence points to the fact that the Caucasoid component in South Asia is primarily of West Asian origin, and the ratio of "West Asia"/"North Europe" components in the region places the origins of that population somewhere between the Northeast Caucasus and the Armenian Plateau in terms of the current inhabitants of West Eurasia.

There is no such thing as ANI, it is an abstraction needed to fit a 2-population model to Indian Cline population. That abstraction is indeed much closer to populations from the West Asian area than to populations from Europe.

I don't know what language Andronovo spoke; there have been several episodes of language replacement in the steppe already. Their language is probably lost forever.

The Westerness of the North Eurasian component certainly speaks against the Proto Indo-Europeans being Eastern Europeans doesn't it?

ANI being close to West Asian populations makes sense since it is mostly West Asian with some of the Atlantic-baltic and the populations of the Caucasus have this exact mix of components.

But in certain runs some of the North Indian participants are like 50% South Asian in addition to their Atlantic-Baltic and West Asian components. So some of this has to be West Eurasian and probably West Eurasian ancestry specific to the region. I was just calling that component ANI but I suppose it would be close to West Asian anyways.

But minus the Asi admixture 70% W Asian and 30% Atlantic Baltic seems ike a good fit since the region is probably like 55% W Asian/~20% Atlantic Baltic/25% other(asi, east asian, mediterranian/sw asian).

What type of phenotype would be associated with these people then(west asian +atlantic/baltic). This question is probably in the pseudoscience range so don't answer if you don't want to. i am just curious. You have helped enough. Thanks.

Slavic makes its first appearance 3 thousand years after the Andronovo culture. The Slavs are latecomers to both the historical scene and the steppe; prior to their eastward expansion, the steppe was inhabited by Iranic-Altaic speakers.

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